X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makecontigscommand.cpp;h=85b6a8fdcbacf1ca1ee5b471b2142480ecf5da48;hb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1;hp=c8f20f10eed04c59df0aa27c136029e43713579e;hpb=67ea6ccd74dbd64828d31b952808255f206364ff;p=mothur.git

diff --git a/makecontigscommand.cpp b/makecontigscommand.cpp
index c8f20f1..85b6a8f 100644
--- a/makecontigscommand.cpp
+++ b/makecontigscommand.cpp
@@ -1681,7 +1681,7 @@ bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, stri
 					// get rest of line in case there is a primer name
 					while (!in.eof())	{	
 						char c = in.get(); 
-						if (c == 10 || c == 13){	break;	}
+						if (c == 10 || c == 13 || c == -1){	break;	}
 						else if (c == 32 || c == 9){;} //space or tab
 						else { 	group += c;  }
 					} 
@@ -1713,7 +1713,7 @@ bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, stri
                     group = "";
                     while (!in.eof())	{	
 						char c = in.get(); 
-						if (c == 10 || c == 13){	break;	}
+						if (c == 10 || c == 13 || c == -1){	break;	}
 						else if (c == 32 || c == 9){;} //space or tab
 						else { 	group += c;  }
 					}